Code

Tims tof reader#812

Code

Merged

trishorts merged 87 commits intosmith-chem-wisc:mastersmith-chem-wisc/mzLib:masterfrom Alexander-Sol:timsTOFReaderAlexander-Sol/mzLib:timsTOFReaderCopy head branch name to clipboardJan 19, 2025

+2,081-30

Commits

Commits on Nov 18, 2023

• Started frameProxy class

  Alexander-Sol

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  d5cb13f

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Commits on Nov 20, 2023

• Added conversion functions

  Alexander-Sol

  committed
  d001aca

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Commits on Nov 21, 2023

• Added useful functions to FrameProxy

  Alexander-Sol

  committed
  ef23825

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Commits on Nov 22, 2023

• Started methods for scan building, added new MsDataScan class

  Alexander-Sol

  committed
  93d47c6

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• Minor

  Alexander-Sol

  committed
  5675c5c

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Commits on Nov 29, 2023

• TimsTof reader is working!!!

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  Alexander-Sol

  committed
  a574388

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Commits on Nov 30, 2023

• minor

  Alexander-Sol

  committed
  57a061f

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• Fixed merge conflicts

  Alexander-Sol

  committed
  b59ee70

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• Fixed merge booboo

  Alexander-Sol

  committed
  b8fe87c

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Commits on Dec 7, 2023

• TimsDataScan is missing

  Alexander-Sol

  committed
  6dd39d1

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Commits on Dec 8, 2023

• started spectra addition stuff

  Alexander-Sol

  committed
  a9df28f

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Commits on Dec 9, 2023

• Finished spectraMerger class

  Alexander-Sol

  committed
  1ae9727

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Commits on Jan 12, 2024

• Reader reads in + merges all spectra/scans

  Alexander-Sol

  committed
  5632fa0

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Commits on Jan 13, 2024

• Parallelized, but made it worse

  Alexander-Sol

  committed
  91096ee

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Commits on Jan 16, 2024

• Changed MS2 merger to keep list nodes

  Alexander-Sol

  committed
  23e0a8c

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• reverted MS2 merger changes

  Alexander-Sol

  committed
  7e2177e

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Commits on Jan 30, 2024

• unsure

  Alexander-Sol

  committed
  be4ca1b

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Commits on Apr 17, 2024

• Merge branch 'master' into timsTOFReader

  Alexander-Sol

  authored
  b038767

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Commits on Jun 19, 2024

• Merge branch 'timsTOFReader' of https://github.com/Alexander-Sol/mzLib into timsTOFReader

  Alexander-Sol

  committed
  cad6bae

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• Working but slowly

  Alexander-Sol

  committed
  e766260

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• idk

  Alexander-Sol

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  0236386

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Commits on Jun 20, 2024

• Added support for missing Pasef scans, missing precursors

  Alexander-Sol

  committed
  4ca6874

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Commits on Jul 8, 2024

• Making progress

  Alexander-Sol

  committed
  94beb90

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Commits on Jul 9, 2024

• Seems to be working

  Alexander-Sol

  committed
  952f021

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Commits on Jul 10, 2024

• Removed empty scans

  Alexander-Sol

  committed
  1d47d49

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Commits on Sep 15, 2024

• fixed merge conflicts

  Alexander-Sol

  committed
  a9fb8b3

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• Finished timsTof reader, added tests

  Alexander-Sol

  committed
  26285c5

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• Updated timsdata.dll path in DllImport call

  Alexander-Sol

  committed
  d6b9e75

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Commits on Sep 16, 2024

• Fixed broken tests

  Alexander-Sol

  committed
  f6c740a

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• changed bruker dll location in directory

  Alexander-Sol

  committed
  21aefc9

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• updated references

  Alexander-Sol

  committed
  6417ef4

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• updated github actions

  Alexander-Sol

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  26d2058

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• added depndencies

  Alexander-Sol

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  fa6be72

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• edited workflow

  Alexander-Sol

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  b1a36f3

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• workflow

  Alexander-Sol

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  aeae7c1

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Commits on Sep 18, 2024

• mzLookup table

  Alexander-Sol

  committed
  8c9ae65

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Commits on Sep 20, 2024

• memoization of mz values, commented out, local tests

  Alexander-Sol

  committed
  da39272

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Commits on Dec 2, 2024

• not immediately clear

  Alexander-Sol

  committed
  c350aa9

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Commits on Dec 3, 2024

• finished index based spectra handling

  Alexander-Sol

  committed
  276ce1a

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• Improved parallelization

  Alexander-Sol

  committed
  a2eeffc

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• Finished performance improvements

  Alexander-Sol

  committed
  f2ef052

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Commits on Dec 4, 2024

• Centroiding on mzs, not indices

  Alexander-Sol

  committed
  df8ac01

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Commits on Dec 5, 2024

• Fixed tests

  Alexander-Sol

  committed
  3b1e61d

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• fixed merge conflicts

  Alexander-Sol

  committed
  597b175

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• Fixed bugs

  Alexander-Sol

  committed
  072f2da

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• Updated workflow

  Alexander-Sol

  committed
  fc44991

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• Created copies of dlls

  Alexander-Sol

  committed
  17b9103

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• Reorganized readers

  Alexander-Sol

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  e8be6d8

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• idk

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  ec1e7c6

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• Updated worklfow

  Alexander-Sol

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  8360603

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• Updated worklfow

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  9de6bfe

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• Updated worklfow

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  db69e2c

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• Updated worklfow

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  6b652d0

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• Updated worklfow

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  55c6094

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• Updated worklfow

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  03bd993

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• Updated worklfow

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  607a9f1

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• included dependencies

  Alexander-Sol

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  323046b

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Commits on Dec 6, 2024

• Pretty sure I just broke things

  Alexander-Sol

  committed
  8033e37

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• idk

  Alexander-Sol

  committed
  ec1cf8e

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• Deleted unused code, dlls

  Alexander-Sol

  committed
  d20d2c1

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Commits on Dec 9, 2024

• Fixed index out of range issue

  Alexander-Sol

  committed
  827318c

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• Idk

  Alexander-Sol

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  253d258

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• Fixed issue where filtering was not performed

  Alexander-Sol

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  dd4b1d3

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Commits on Dec 13, 2024

• Things work!

  Alexander-Sol

  committed
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Commits on Dec 17, 2024

• pre-size lists

  Alexander-Sol

  committed
  c536184

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Commits on Jan 6, 2025

• Change ProteinDBWriter in the wrong branch

  Alexander-Sol

  committed
  b59cc57

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Commits on Jan 15, 2025

• Fixed merge conflicts

  Alexander-Sol

  committed
  2c8cfea

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• Refactoring so sql calls have their own methods

  Alexander-Sol

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  e120c82

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Commits on Jan 16, 2025

• Added functions for dynamic connections, associated tests

  Alexander-Sol

  committed
  9433a17

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• Extended test coverage

  Alexander-Sol

  committed
  3edf877

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• Minor

  Alexander-Sol

  committed
  52a25b1

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• Fixed merge conflicts

  Alexander-Sol

  committed
  cb28554

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• Implemented try/finally blocks for calls to Marshal

  Alexander-Sol

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  d13c67a

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• Deleted unused code, extended tests

  Alexander-Sol

  committed
  dc18bf0

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• Fixed double deallocation of memory

  Alexander-Sol

  committed
  7a67440

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• Deleted unintended changes

  Alexander-Sol

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  8acc4d7

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• Deleted unused code

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  330eac7

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• Deleted unintended changes

  Alexander-Sol

  committed
  4695762

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• Edited workflow

  Alexander-Sol

  committed
  12503cb

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• Nixed CSV helper

  Alexander-Sol

  committed
  b6193fd

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• Fixed mobilityscan index issues

  Alexander-Sol

  committed
  c865b20

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• Added comments

  Alexander-Sol

  committed
  8854769

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Commits on Jan 17, 2025

• Added comments, addressed concerns

  Alexander-Sol

  committed
  362f654

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• Fixed failing test

  Alexander-Sol

  committed
  4d72987

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• Merge branch 'master' into timsTOFReader

  trishorts

  authored
  015f8d8

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Commits on Jan 18, 2025

• Merge branch 'master' into timsTOFReader

  nbollis

  authored
  f0e20d5

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• Merge branch 'master' into timsTOFReader

  trishorts

  authored
  a373255

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